phyloseq：使用tax_glom前后otu计数的差异

发布于 2025-01-19 17:45:17 字数 511 浏览 4 评论 0原文

也许我错过了tax_glom如何工作的一些内容，但由于我在这里或网络上的其他地方都没有找到任何信息，也许这里有人可以提供帮助。我不提供数据，但可以根据要求提供。下面是突出显示我遇到的问题的代码：

colSums(CYANO%>%otu_table())

CYANO_gen <- CYANO %>%
  tax_glom(taxrank = "Genus")
colSums(CYANO_gen%>%otu_table())

CYANO 是一个 phyloseq 对象，我想将其聚集在属等级上，但我注意到数据可视化中不存在样本（名为 100）。这促使我检查问题发生在哪里。 54 个样本中有 7 个存在差异，如所附图片的最后一行所示，很奇怪不是吗？

上面的代码给出的结果和另外 2 行强调了差异的重要性以及事实并不总是如此案例

谢谢，纪尧姆

原文

Maybe I missed something in how tax_glom works but as I did not find any info here nor elsewhere on the web, maybe someone here can help.
I do not provide data but I can on request. Here is the code highlighting the issue I have

colSums(CYANO%>%otu_table())

CYANO_gen <- CYANO %>%
  tax_glom(taxrank = "Genus")
colSums(CYANO_gen%>%otu_table())

CYANO is a phyloseq object that I wanted to agglomerate at the Genus rank but I noticed that a sample (named 100) was not present in a dataviz. This led me to check where the issue happened. 7 samples out of 54 present discrepancies as shown in the last line of the attached image, weird isn't it?

Results given by the code above and 2 additional lines which highlight the importance of discrepancies and the fact that this is not always the case

Thank, Guillaume

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